"Look" means to look away, to look into the distance, to look out. "Autumn water" originally refers to the lake water or rain water in autumn, but in the idiom of "looking through autumn water", it means that one's eyes are as crystal as autumn water.
This idiom is a positive one, which is generally used to describe the deep longing of an affectionate woman for her lover. It is often seen in classical literature, especially in Song lyrics and Yuan operas. Looking through the waters of autumn is from the Yuan dynasty Wang Shifu's "The West Wing", the third book of the second fold: If you don't go ah, looking through his full of autumn water, knit damage his light spring mountains.